The jacktree genome and population genomics provides insights for the mechanisms of the germination obstacle and the conservation of endangered ornamental plants

Abstract

Sinojackia Hu represents the first woody genus described by Chinese botanists, with all species classified as endangered ornamental plants endemic to China. Their characteristic spindle-shaped fruits confer high ornamental value to the plants, making them favored in gardens and parks. Nevertheless, the fruits likely pose a germination obstacle, contributing to the endangered status of this lineage. Here we report the chromosome-scale genome of S. xylocarpa, and explore the mechanisms underlying its endangered status, as well as its population dynamics throughout evolution. Population genomic analysis has indicated that S. xylocarpa experienced a bottleneck effect following the recent glacial period, leading to a continuous population reduction. Examination of the pericarp composition across six stages of fruit development revealed a consistent increase in the accumulation of lignin and fiber content, responsible for the sturdiness of mature fruits’ pericarps. At molecular level, enhanced gene expression in the biosynthesis of lignin, cellulose and hemicellulose was detected in pericarps. Therefore, we conclude that the highly lignified and fibrotic pericarps of S. xylocarpa, which inhibit its seed germination, should be its threatening mechanism, thus proposing corresponding strategies for improved conservation and restoration. This study serves as a seminal contribution to conservation biology, offering valuable insights for the study of other endangered ornamental plants.

Acknowledgements

We acknowledge Shi-Jing Sun at College of Materials Science and Engineering, Nanjing Forestry University for assistance in lignin determination. We also thank Xiao-Gang Xu at College of Life Sciences, Nanjing Forestry University, and Dao-Liang Yan at School of Forestry and Biotechnology Zhejiang A&F University, for help in collecting plant samples. We sincerely thank Wen-Tai Dai from the Institute of Soil Science, Chinese Academy of Sciences, for his assistance in soil data collection. We also appreciate the advice on data analysis provided by Jie-Yu Wang at China National Genebank (CNGB), Shenzhen, Cheng-ao Yang at College of Horticulture, Nanjing Agricultural University, and Yu-Peng Sang at College of Life Sciences, Sichuan University. We also acknowledge the data support from ‘National Earth System Science Data Center (https://www.geodata.cn)’. This work was financially supported by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

Author contributions

Y.-F.D. and J.-Y.X. conceived and designed the project. X.-F.W., S.Z., Y.-X.L., D.-W.Z., Z.-F.W., and J.G. conducted bioinformatic analyses. Y.-X.L., D.-W.Z., and S.-L.L. performed anatomical experiments and lignin determination. S.-L.L., Y.-F.S., Y.Y., X.-G.Y., and M.Z. collected the plant materials. S.Z., X.-F.W., Y.-X.L., Z.-F.W., and J.-Y.X. drafted the manuscript. All authors contributed to and approved the final manuscript.

Data availability

Assembled genome, DNA resequencing, and RNA sequencing data for S. xylocarpa are accessible from NGDC (National Genomics Data Center, https://ngdc.cncb.ac.cn/) under BioProject no. PRJCA016116, consisting of GWH (genome warehouse) no. GWHCBFM00000000, and GSA (genome sequence archive) no. CRA010572 and CRA016108, respectively. All relevant data can be found within the manuscript and its supporting materials.

Conflict of interest statement

The authors declare that there is no conflict of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

References

[1] Hu HH. Sinojackia, a new genus of Styracaceae from southeastern China. J Arnold Arbor. 1928; 9 :130-1

[2] Xiao-Hong Y, Qi-Gang Y, Ji-Wen G. et al. A new species of Sinojackia (Styracaceae) from Hubei, Central China. Novon. 2007; 17 : 138-40

[3] Wu Y, Bao WQ, Hu H. et al. Mechanical constraints in the endosperm and endocarp are major causes of dormancy in Sinojackia xylocarpa Hu (Styracaceae) seeds. J Plant Growth Regul. 2023; 42 :644-57

[4] Theissinger K, Fernandes C, Formenti G. et al. How genomics can help biodiversity conservation. Trends Genet. 2023; 39 : 545-59

[5] Yang Y, Ma T, Wang Z. et al. Genomic effects of population collapse in a critically endangered ironwood tree Ostrya rehderiana. Nat Commun. 2018; 9 :5449

[6] Chen Y, Ma T, Zhang L. et al. Genomic analyses of a ‘living fossil’: the endangered dove-tree. Mol Ecol Resour. 2020; 20 : 756-69

[7] Yang J, Wariss HM, Tao L. et al. De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China. Giga-science. 2019; 8 :giz085

[8] Ma Y, Liu D, Wariss HM. et al. Demographic history and identification of threats revealed by population genomic analysis provide insights into conservation for an endangered maple. Mol Ecol. 2022; 31 :767-79

[9] Formenti G, Theissinger K, Fernandes C. et al. The era of reference genomes in conservation genomics. Trends Ecol Evol. 2022; 37 :197-202

[10] Yao X, Ye Q, Fritsch PW. et al. Phylogeny of Sinojackia (Styracaceae) based on DNA sequence and microsatellite data: implications for taxonomy and conservation. Ann Bot. 2008; 101 : 651-9

[11] Cai XL, Landis JB, Wang HX. et al. Plastome structure and phylogenetic relationships of Styracaceae (Ericales). BMC EcolEvol. 2021; 21 :103

[12] Wang LL, Zhang Y, Yang YC. et al. The complete chloroplast genome of (Ericales: Styracaceae), an endangered plant species endemic to China. Conserv Genet Resour. 2018; 10 :51-4

[13] Fan J, Fu QC, Liang Z. Complete chloroplast genome sequence and phylogenetic analysis of an endemic plant in Southwest China. Mitochondrial DNA Part B-Resources. 2019; 4 : 1350-1

[14] Dong HJ, Wang HY, Li YL. et al. The complete chloroplast genome sequence of (Styracaceae). Mitochondrial DNA Part B-Resources. 2020; 5 :715-7

[15] Yao X, Zhang J, Ye Q. et al. Fine-scale spatial genetic structure and gene flow in a small, fragmented population of Sinojackiarehderiana (Styracaceae), an endangered tree species endemic to China. Plant Biol (Stuttg). 2011; 13 :401-10

[16] Zhang JJ, Ye QG, Yao XH. et al. Microsatellite diversity and mating system of Sinojackia xylocarpa (Styracaceae), a species extinct in the wild. Biochem Syst Ecol. 2010; 38 :154-9

[17] Zhong TL, Zhao GW, Lou YF. et al. Genetic diversity analysis of Sinojackia microcarpa, a rare tree species endemic in China, based on simple sequence repeat markers. J For Res. 2019; 30 : 847-54

[18] Yang FS, Nie S, Liu H. et al. Chromosome-level genome assembly of a parent species of widely cultivated azaleas. Nat Commun. 2020; 11 :5269

[19] Tang W, Sun X, Yue J. et al. Chromosome-scale genome assembly of kiwifruit Actinidia eriantha with single-molecule sequencing and chromatin interaction mapping. Gigascience. 2019; 8 :giz027

[20] Zhu QG, Xu Y, Yang Y. et al. The persimmon (Diospyros oleifera Cheng) genome provides new insights into the inheritance of astringency and ancestral evolution. Hortic Res. 2019; 6 :138

[21] Wang F, Zhang B, Wen D. et al. Chromosome-scale genome assembly of Camellia sinensis combined with multi-omics provides insights into its responses to infestation with green leafhoppers. Front Plant Sci. 2022; 13 :1004387

[22] Yan M, Fritsch PW, Moore MJ. et al. Plastid phylogenomics resolves infrafamilial relationships of the Styracaceae and sheds light on the backbone relationships of the Ericales. MolPhylogenet Evol. 2018; 121 :198-211

[23] Larson DA, Walker JF, Vargas OM. et al. A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales. Am J Bot. 2020; 107 :773-89

[24] The Angiosperm Phylogeny Group, Chase MW, Christenhusz MJM. et al. An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG IV. Bot J Linn Soc. 2016; 181 :1-20

[25] Kapli P, Yang ZH, Telford MJ. Phylogenetic tree building in the genomic age. Nat Rev Genet. 2020; 21 :428-44

[26] Xia EH, Zhang HB, Sheng J. et al. The tea tree genome provides insights into tea flavor and independent evolution of caffeine biosynthesis. Mol Plant. 2017; 10 :866-77

[27] Wang X, Gao Y, Wu X. et al. High-quality evergreen azalea genome reveals tandem duplication-facilitated low-altitude adaptability and floral scent evolution. Plant Biotechnol J. 2021; 19 :2544-60

[28] Murat F, Armero A, Pont C. et al. Reconstructing the genome of the most recent common ancestor of flowering plants. NatGenet. 2017; 49 :490-6

[29] Storfer A. Gene flow and endangered species translocations: a topic revisited. Biol Conserv. 1999; 87 :173-80

[30] Guo M, Zhang Z, Cheng Y. et al. Comparative population genomics dissects the genetic basis of seven domestication traits in jujube. Hortic Res. 2020; 7 :89

[31] An C, Sheng L, Du X. et al. Overexpression of CmMYB15 provides chrysanthemum resistance to aphids by regulating the biosynthesis of lignin. Hortic Res. 2019; 6 :84

[32] Jiao B, Zhao X, Lu W. et al. The R2R3 MYB transcription factor MYB189 negatively regulates secondary cell wall biosynthesis in Populus. Tree Physiol. 2019; 39 :1187-200

[33] Sun Y, Ren S, Ye S. et al. Identification and functional characterization of PtoMYB055 involved in the regulation of the lignin biosynthesis pathway in Populus tomentosa. Int J Mol Sci. 2020; 21 :4857

[34] Zhang Q, Wang L, Wang Z. et al. The regulation of cell wall lignification and lignin biosynthesis during pigmentation of winter jujube. Hortic Res. 2021; 8 :238

[35] Moore MJ, Soltis PS, Bell CD. et al. Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots. Proc Natl Acad Sci USA. 2010; 107 :4623-8

[36] Li HT, Yi TS, Gao LM. et al. Origin of angiosperms and the puzzle of the Jurassic gap. Nat Plants. 2019; 5 :461-70

[37] Li HT, Luo Y, Gan L. et al. Plastid phylogenomic insights into relationships of all flowering plant families. BMC Biol. 2021; 19 :232

[38] Zeng L, Zhang N, Zhang Q. et al. Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets. New Phytol. 2017; 214 :1338-54

[39] One Thousand Plant Transcriptomes Initiative. One thousand plant transcriptomes and the phylogenomics of green plants. Nature. 2019; 574 :679-85

[40] Yang L, Su D, Chang X. et al. Phylogenomic insights into deep phylogeny of angiosperms based on broad nuclear gene sampling. Plant Commun. 2020; 1 :100027

[41] Toju H, Sota T. Phylogeography and the geographic cline in the armament of a seed-predatory weevil: effects of historical events vs. natural selection from the host plant. Mol Ecol. 2006; 15 :4161-73

[42] Fang L, Xu X, Li J. et al. Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum arme-niacum seed. BMC Genomics. 2020; 21 :524

[43] Xue JY, Li Z, Hu SY. et al. The Saururus chinensis genome provides insights into the evolution of pollination strategies and herbaceousness in magnoliids. Plant J. 2023; 113 : 1021-34

[44] Liu Q, Luo L, Zheng L. Lignins: biosynthesis and biological functions in plants. Int J Mol Sci. 2018; 19 :335

[45] Emonet A, Hay A. Development and diversity of lignin patterns. Plant Physiol. 2022; 190 :31-43

[46] Demura T, Fukuda H. Transcriptional regulation in wood formation. Trends Plant Sci. 2007; 12 :64-70

[47] Bonawitz ND, Chapple C. The genetics of lignin biosynthesis: connecting genotype to phenotype. Annu Rev Genet. 2010; 44 : 337-63

[48] Ding Y, Yu S, Wang J. et al. Comparative transcriptomic analysis of seed coats with high and low lignin contents reveals lignin and flavonoid biosynthesis in Brassica napus. BMC Plant Biol. 2021; 21 :246

[49] Atiwesh G, Parrish CC, Banoub J. et al. Lignin degradation by microorganisms: A review. Biotechnol Prog. 2022; 38 :e3226

[50] Zeng S, Huang W, Wu K. et al. In vitro propagation of Paphiopedilum orchids. Crit Rev Biotechnol. 2016; 36 :521-34

[51] Rao SS, Huntley MH, Durand NC. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014; 159 :1665-80

[52] Ranallo-Benavidez TR, Jaron KS, Schatz MC. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat Commun. 2020; 11 :1432

[53] Cheng H, Concepcion GT, Feng X. et al. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021; 18 :170-5

[54] Servant N, Varoquaux N, Lajoie BR. et al. HiC-pro: an optimized and flexible pipeline for hi-C data processing. Genome Biol. 2015; 16 :259

[55] Burton JN, Adey A, Patwardhan RP. et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotechnol. 2013; 31 :1119-25

[56] Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25 :1754-60

[57] Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics. 2007; 23 :1061-7

[58] Simao FA, Waterhouse RM, Ioannidis P. et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31 :3210-2

[59] Kim D, Paggi JM, Park C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotech-nol. 2019; 37 :907-15

[60] Pertea M, Kim D, Pertea GM. et al. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016; 11 :1650-67

[61] Keilwagen J, Hartung F, Grau J. GeMoMa: homology-based gene prediction utilizing intron position conservation and RNA-seq data. Methods Mol Biol. 2019; 1962 :161-77

[62] Hoff KJ, Stanke M. Predicting genes in single genomes with AUGUSTUS. Curr Protoc Bioinformatics. 2019; 65 :e57

[63] Haas BJ, Salzberg SL, Zhu W. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol. 2008; 9 :R7

[64] Haas BJ, Delcher AL, Mount SM. et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 2003; 31 :5654-66

[65] Buchfink B, Reuter K, Drost HG. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods. 2021; 18 :366-8

[66] Huerta-Cepas J, Szklarczyk D, Heller D. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 2019; 47 :D309-14

[67] Mistry J, Chuguransky S, Williams L. et al. Pfam:the protein families database in 2021. Nucleic Acids Res. 2021; 49 :D412-9

[68] Ellinghaus D, Kurtz S, Willhoeft U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics. 2008; 9 :18

[69] Ou S, Jiang N. LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons. Mob DNA. 2019; 10 :48

[70] Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019; 20 :238

[71] Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32 : 1792-7

[72] Nguyen LT, Schmidt HA, von Haeseler A. et al. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015; 32 :268-74

[73] Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007; 24 :1586-91

[74] Mendes FK, Vanderpool D, Fulton B. et al. CAFE 5 models variation in evolutionary rates among gene families. Bioinformatics. 2021; 36 :5516-8

[75] Zwaenepoel A, Van de Peer Y. Wgd-simple command line tools for the analysis of ancient whole-genome duplications. Bioinformatics. 2019; 35 :2153-5

[76] Camacho C, Coulouris G, Avagyan V. et al. BLAST + : architecture and applications. BMC Bioinformatics. 2009; 10 :421

[77] Rozewicki J, Li S, Amada KM. et al. MAFFT-DASH: integrated protein sequence and structural alignment. Nucleic Acids Res. 2019; 47 :W5-10

[78] Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009; 26 :1641-50

[79] Sun P, Jiao B, Yang Y. et al. WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes. Mol Plant. 2022; 15 :1841-51

[80] Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012; 9 :357-9

[81] Florea L, Song L, Salzberg SL. Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues. F1000Res. 2013; 2 :188

[82] Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioin-formatics. 2011; 12 :323

[83] Chen C, Chen H, Zhang Y. et al. TBtools: An integrative toolkit developed for interactive analyses of big biological data. MolPlant. 2020; 13 :1194-202

[84] Xiao R, Zhang C, Guo X. et al. MYB transcription factors and its regulation in secondary cell wall formation and lignin biosynthesis during xylem development. Int J Mol Sci. 2021; 22 :3560

[85] Yao T, Feng K, Xie M. et al. Phylogenetic occurrence of the phenylpropanoid pathway and lignin biosynthesis in plants. Front Plant Sci. 2021; 12 :704697

[86] Oliver T, Schmidt B, Nathan D. et al. Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW. Bioinformatics. 2005; 21 :3431-2

[87] Minh BQ, Schmidt HA, Chernomor O. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020; 37 :1530-4

[88] Chen S, Zhou Y, Chen Y. et al. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018; 34 :i884-90

[89] Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv: Genomics. 2013; arXiv:1303.3997, preprint: not peer reviewed

[90] Danecek P, Bonfield JK, Liddle J. et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021; 10 :giab008

[91] McKenna A, Hanna M, Banks E. et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010; 20 :1297-303

[92] DePristo MA, Banks E, Poplin R. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011; 43 :491-8

[93] Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010; 38 :e164

[94] Purcell S, Neale B, Todd-Brown K. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007; 81 :559-75

[95] Felsenstein J. PHYLIP (Phylogeny Inference Package) Version 3.6. Department of Genome Sciences. Seattle: University of Washington; 2005:

[96] Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009; 19 : 1655-64

[97] Zhang C, Dong SS, Xu JY. et al. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics. 2019; 35 :1786-8

[98] Yi HQ, Wang JY, Wang J. et al. Genomic insights into inter- and intraspecific mating system shifts in Primulina. Mol Ecol. 2022; 31 :5699-713

[99] Li H, Durbin R. Inference of human population history from individual whole-genome sequences. Nature. 2011; 475 : 493-6

[100] Chen H, Patterson N, Reich D. Population differentiation as a test for selective sweeps. Genome Res. 2010; 20 :393-402

[101] Excoffier L, Dupanloup I, Huerta-Sanchez E. et al. Robust demographic inference from genomic and SNP data. PLoS Genet. 2013; 9 :e1003905

[102] Frichot E, François O. LEA: An R package for landscape and ecological association studies. Methods Ecol Evol. 2015; 6 : 925-9

[103] van den Wollenberg AL. Redundancy analysis an alternative for canonical correlation analysis. Psychometrika. 1977; 42 : 207-19